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SUMMARY      ANALYSIS
The analysis detected some serious issues.   Details »

Estimated Number of Cells

20,717

Post-Normalization Mean Reads per Cell

13,613

Median Genes per Cell

2,372
Pre-Normalization Number of Reads
Total number of read pairs that were assigned to these libraries in demultiplexing.
Post-Normalization Number of Reads
Number of read pairs after normalizing for depth among multiple libraries.

Sequencing

Pre-Normalization Number of Reads 350,739,155
Post-Normalization Number of Reads 282,020,608
LN1 AS38 Fraction of Reads Kept
The fraction of reads kept for this input sample, after normalizing depth across samples to reduce batch effects.
LN2 AS59 3 Fraction of Reads Kept
The fraction of reads kept for this input sample, after normalizing depth across samples to reduce batch effects.
LN3 AS74 Fraction of Reads Kept
The fraction of reads kept for this input sample, after normalizing depth across samples to reduce batch effects.
LN4 AS79 Fraction of Reads Kept
The fraction of reads kept for this input sample, after normalizing depth across samples to reduce batch effects.
LN1 AS38 Pre-Normalization Total Reads per Cell
The mean number of total sequencing reads per cell in this input sample, prior to depth normalization.
LN2 AS59 3 Pre-Normalization Total Reads per Cell
The mean number of total sequencing reads per cell in this input sample, prior to depth normalization.
LN3 AS74 Pre-Normalization Total Reads per Cell
The mean number of total sequencing reads per cell in this input sample, prior to depth normalization.
LN4 AS79 Pre-Normalization Total Reads per Cell
The mean number of total sequencing reads per cell in this input sample, prior to depth normalization.
LN1 AS38 Pre-Normalization Confidently Mapped Barcoded Reads per Cell
The mean number of confidently-mapped-to-transcriptome, valid-barcode reads per cell in this input sample, prior to depth normalization.
LN2 AS59 3 Pre-Normalization Confidently Mapped Barcoded Reads per Cell
The mean number of confidently-mapped-to-transcriptome, valid-barcode reads per cell in this input sample, prior to depth normalization.
LN3 AS74 Pre-Normalization Confidently Mapped Barcoded Reads per Cell
The mean number of confidently-mapped-to-transcriptome, valid-barcode reads per cell in this input sample, prior to depth normalization.
LN4 AS79 Pre-Normalization Confidently Mapped Barcoded Reads per Cell
The mean number of confidently-mapped-to-transcriptome, valid-barcode reads per cell in this input sample, prior to depth normalization.

Aggregation

LN1 AS38 Fraction of Reads Kept 89.7%
LN2 AS59 3 Fraction of Reads Kept 69.3%
LN3 AS74 Fraction of Reads Kept 100.0%
LN4 AS79 Fraction of Reads Kept 62.8%
LN1 AS38 Pre-Normalization Total Reads per Cell 15,149
LN2 AS59 3 Pre-Normalization Total Reads per Cell 19,906
LN3 AS74 Pre-Normalization Total Reads per Cell 13,893
LN4 AS79 Pre-Normalization Total Reads per Cell 20,872
LN1 AS38 Pre-Normalization Confidently Mapped Barcoded Reads per Cell 7,753
LN2 AS59 3 Pre-Normalization Confidently Mapped Barcoded Reads per Cell 10,039
LN3 AS74 Pre-Normalization Confidently Mapped Barcoded Reads per Cell 6,952
LN4 AS79 Pre-Normalization Confidently Mapped Barcoded Reads per Cell 11,075
 
Estimated Number of Cells
The total number of barcodes associated with cell-containing partitions, estimated from the barcode count distribution.
Fraction Reads in Cells
The fraction of valid-barcode, confidently-mapped-to-transcriptome reads with cell-associated barcodes.
Pre-Normalization Mean Reads per Cell
The total number of sequenced reads divided by the number of barcodes associated with cell-containing partitions.
Post-Normalization Mean Reads per Cell
The total number of (depth-normalized) reads divided by the number of barcodes associated with cell-containing partitions.
Median Genes per Cell
The median number of genes detected per cell-associated barcode. Detection is defined as the presence of at least 1 UMI count.
Median UMI Counts per Cell
The median number of UMI counts per cell-associated barcode.

Cells

Estimated Number of Cells 20,717
Fraction Reads in Cells 94.3%
Pre-Normalization Mean Reads per Cell 16,930
Post-Normalization Mean Reads per Cell 13,613
Median Genes per Cell 2,372
Median UMI Counts per Cell 6,401

Sample

Name LN_aggr
Description
Transcriptome GRCh38
Chemistry Single Cell 3' v3
Cell Ranger Version 3.0.1

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